Gene expression profiles in neurological tissues during West Nile virus infection: a critical meta-analysis

BMC Genomics
Robin KoschKlaus Jung

Abstract

Infections with the West Nile virus (WNV) can attack neurological tissues in the host and alter gene expression levels therein. Several individual studies have analyzed these changes in the transcriptome based on measurements with DNA microarrays. Individual microarray studies produce a high-dimensional data structure with the number of studied genes exceeding the available sample size by far. Therefore, the level of scientific evidence of these studies is rather low and results can remain uncertain. Furthermore, the individual studies concentrate on different types of tissues or different time points after infection. A general statement regarding the transcriptional changes through WNV infection in neurological tissues is therefore hard to make. We screened public databases for transcriptome expression studies related to WNV infections and used different analysis pipelines to perform meta-analyses of these data with the goal of obtaining more stable results and increasing the level of evidence. We generated new lists of genes differentially expressed between WNV infected neurological tissues and control samples. A comparison with these genes to findings of a meta-analysis of immunological tissues is performed to figure out tis...Continue Reading

References

Sep 16, 1998·Lancet·T F TsaiN I Nedelcu
Jan 4, 2001·Microbes and Infection·R C Russell, D E Dwyer
Mar 27, 2001·Emerging Infectious Diseases·A E PlatonovV I Pokrovskii
Jun 16, 2001·The New England Journal of Medicine·D NashUNKNOWN 1999 West Nile Outbreak Response Working Group
Oct 5, 2001·Clinical Microbiology Reviews·C E Samuel
Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
Jan 19, 2002·Annals of the New York Academy of Sciences·V DeubelP Desprès
Jul 16, 2002·Annual Review of Biomedical Engineering·Michael J Heller
Sep 7, 2002·The Lancet Infectious Diseases·Grant L CampbellDuane J Gubler
Jul 12, 2003·Bioinformatics·Jung Kyoon ChoiOok Joon Yoo
Jul 24, 2003·JAMA : the Journal of the American Medical Association·James J SejvarLyle R Petersen
Dec 21, 2004·Nucleic Acids Research·H ParkinsonA Brazma
May 12, 2005·Virus Research·Susanne Kramer-HämmerleRuth Brack-Werner
Aug 17, 2005·Journal of Virology·Robyn S KleinMichael S Diamond
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Nov 29, 2005·Veterinary Immunology and Immunopathology·David Garcia-TapiaSteven B Kleiboeker
Apr 25, 2006·Biostatistics·W Evan JohnsonAriel Rabinovic
Jun 27, 2006·Journal of Neurovirology·Elizabeth A Hunsperger, John T Roehrig
Aug 30, 2006·Methods in Enzymology·Dennise D Dalma-WeiszhauszC Garrett Miyada
May 15, 2007·Bioinformatics·Sean Davis, Paul S Meltzer
Jul 18, 2008·Journal of Virology·Penghua WangErol Fikrig
Sep 5, 2008·PLoS Medicine·Adaikalavan RamasamyDouglas G Altman
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Jan 17, 2009·The Medical Clinics of North America·Lyle R Petersen, Edward B Hayes
Jan 29, 2009·Nature Genetics·John P A IoannidisVera van Noort
Feb 11, 2009·Journal of Interferon & Cytokine Research : the Official Journal of the International Society for Interferon and Cytokine Research·Jesper MelchjorsenRune Hartmann
Jul 25, 2009·Bioinformatics·Guillemette MarotFlorence Jaffrézic
Dec 17, 2010·The Journal of Investigative Dermatology·Dov HershkovitzEli Sprecher
Apr 30, 2011·BMC Bioinformatics·Andreas LehaKlaus Jung
Sep 2, 2011·Journal of Virology·Kristy J SzretterMichael S Diamond
Dec 17, 2011·Emerging Infectious Diseases·Ignacio García-BocanegraAntonio Arenas
Jan 21, 2012·Nucleic Acids Research·George C TsengEleanor Feingold
Apr 21, 2012·Emerging Infectious Diseases·Melinda J FrostPeter D Kirkland
Sep 29, 2012·Emerging Infectious Diseases·Jörg Schultze-AmbergerJonas Schmidt-Chanasit
Dec 15, 2012·Nature Reviews. Immunology·Michael S Diamond, Michael Farzan
Jun 14, 2013·BMC Evolutionary Biology·Ana Lemos de MatosPedro J Esteves
Sep 24, 2013·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Martin GabrielJonas Schmidt-Chanasit

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE77192

Methods Mentioned

BETA
RNA-seq
chips
PCA

Software Mentioned

package ‘
package ‘ minet ’
MetaMA ’ R - package
R
ComBat
limma
RStudio
limma ’
GEOquery
GSEA

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.